Man, sounds like you've got a tough one. I'd have to hear the noise before I could offer any more advice.
I think the master links that are braded together are the best. There are links available that are assembled with c-clips. They are tiny and easy to drop so do yourself a favor and stuff several rags rag under it when both doing and undoing either type of master link.
I wouldn't use the new link to wind it in. You only want to stretch the new circlip once to put it on. I usually use the link I cut out to break the chain. One thing to note is that the endplates on the chain are press fit, not slip fit so you'd better have at least one if not two good pair of channel lock pliers handy to press it on.